A strategy for oligonucleotide microarray probe reduction

Alena A Antipova¹^,2, Pablo Tamayo¹ and Todd R Golub¹^,3

¹Center for Genome Research, Whitehead Institute/Massachusetts Institute of Technology, Cambridge, MA 02139, USA

²Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

³Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

author email corresponding author email

Genome Biology 2002, 3:research0073.1-0073.4doi:10.1186/gb-2002-3-12-research0073


Published:	25 November 2002

Subject areas: Bioinformatics, Cancer, Genome studies

Abstract

Background

One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design.

Results

The methodology has been tested on a dataset comprising 317 Affymetrix HuGeneFL GeneChips. The performance of the original and reduced probe sets was compared in four cancer-classification problems. The results of these comparisons show that reduction of the probe set by 95% does not dramatically affect performance, and thus illustrate the feasibility of substantially reducing probe numbers without significantly compromising sensitivity and specificity of detection.

Conclusions

The strategy described here is potentially useful for designing small, limited-probe genome-wide arrays for screening applications.